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1.
Cell ; 177(2): 463-477.e15, 2019 04 04.
Artigo em Inglês | MEDLINE | ID: mdl-30951672

RESUMO

To develop a map of cell-cell communication mediated by extracellular RNA (exRNA), the NIH Extracellular RNA Communication Consortium created the exRNA Atlas resource (https://exrna-atlas.org). The Atlas version 4P1 hosts 5,309 exRNA-seq and exRNA qPCR profiles from 19 studies and a suite of analysis and visualization tools. To analyze variation between profiles, we apply computational deconvolution. The analysis leads to a model with six exRNA cargo types (CT1, CT2, CT3A, CT3B, CT3C, CT4), each detectable in multiple biofluids (serum, plasma, CSF, saliva, urine). Five of the cargo types associate with known vesicular and non-vesicular (lipoprotein and ribonucleoprotein) exRNA carriers. To validate utility of this model, we re-analyze an exercise response study by deconvolution to identify physiologically relevant response pathways that were not detected previously. To enable wide application of this model, as part of the exRNA Atlas resource, we provide tools for deconvolution and analysis of user-provided case-control studies.


Assuntos
Comunicação Celular/fisiologia , RNA/metabolismo , Adulto , Líquidos Corporais/química , Ácidos Nucleicos Livres/metabolismo , MicroRNA Circulante/metabolismo , Vesículas Extracelulares/metabolismo , Feminino , Humanos , Masculino , Reprodutibilidade dos Testes , Análise de Sequência de RNA/métodos , Software
2.
Am J Hum Genet ; 111(1): 133-149, 2024 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-38181730

RESUMO

Bulk-tissue molecular quantitative trait loci (QTLs) have been the starting point for interpreting disease-associated variants, and context-specific QTLs show particular relevance for disease. Here, we present the results of mapping interaction QTLs (iQTLs) for cell type, age, and other phenotypic variables in multi-omic, longitudinal data from the blood of individuals of diverse ancestries. By modeling the interaction between genotype and estimated cell-type proportions, we demonstrate that cell-type iQTLs could be considered as proxies for cell-type-specific QTL effects, particularly for the most abundant cell type in the tissue. The interpretation of age iQTLs, however, warrants caution because the moderation effect of age on the genotype and molecular phenotype association could be mediated by changes in cell-type composition. Finally, we show that cell-type iQTLs contribute to cell-type-specific enrichment of diseases that, in combination with additional functional data, could guide future functional studies. Overall, this study highlights the use of iQTLs to gain insights into the context specificity of regulatory effects.


Assuntos
Regulação da Expressão Gênica , Locos de Características Quantitativas , Humanos , Locos de Características Quantitativas/genética , Genótipo , Fenótipo
3.
Proc Natl Acad Sci U S A ; 120(40): e2305961120, 2023 10 03.
Artigo em Inglês | MEDLINE | ID: mdl-37751556

RESUMO

α-lipoic acid (LA) is an essential cofactor for mitochondrial dehydrogenases and is required for cell growth, metabolic fuel production, and antioxidant defense. In vitro, LA binds copper (Cu) with high affinity and as an endogenous membrane permeable metabolite could be advantageous in mitigating the consequences of Cu overload in human diseases. We tested this hypothesis in 3T3-L1 preadipocytes with inactivated Cu transporter Atp7a; these cells accumulate Cu and show morphologic changes and mitochondria impairment. Treatment with LA corrected the morphology of Atp7a-/- cells similar to the Cu chelator bathocuproinedisulfonate (BCS) and improved mitochondria function; however, the mechanisms of LA and BCS action were different. Unlike BCS, LA did not decrease intracellular Cu but instead increased selenium levels that were low in Atp7a-/- cells. Proteome analysis confirmed distinct cell responses to these compounds and identified upregulation of selenoproteins as the major effect of LA on preadipocytes. Upregulation of selenoproteins was associated with an improved GSH:GSSG ratio in cellular compartments, which was lowered by elevated Cu, and reversal of protein oxidation. Thus, LA diminishes toxic effects of elevated Cu by improving cellular redox environment. We also show that selenium levels are decreased in tissues of a Wilson disease animal model, especially in the liver, making LA an attractive candidate for supplemental treatment of this disease.


Assuntos
Selênio , Ácido Tióctico , Animais , Humanos , Ácido Tióctico/farmacologia , Cobre , Selênio/farmacologia , Oxirredução , Selenoproteínas/genética
4.
Proc Natl Acad Sci U S A ; 119(49): e2201337119, 2022 12 06.
Artigo em Inglês | MEDLINE | ID: mdl-36445963

RESUMO

We present the design of a passive wireless communication method that does not rely on ambient or generated RF sources. Instead, the method modulates the Johnson (thermal) noise of a resistor to transmit information bits wirelessly. By selectively connecting or disconnecting a matched resistor to an antenna, the system can achieve data rates of up to 26 bps and distances of up to 7.3 m. This communication method operates at very low power, similar to that of an RFID tag, with the advantage of not requiring a preexisting RF signal to reflect.


Assuntos
Comunicação
5.
Proc Biol Sci ; 291(2016): 20232749, 2024 Feb 14.
Artigo em Inglês | MEDLINE | ID: mdl-38320605

RESUMO

Ecological communities can be stable over multiple generations, or rapidly shift into structurally and functionally different configurations. In kelp forest ecosystems, overgrazing by sea urchins can abruptly shift forests into alternative states that are void of macroalgae and primarily dominated by actively grazing sea urchins. Beginning in 2014, a sea urchin outbreak along the central coast of California resulted in a patchy mosaic of remnant forests interspersed with sea urchin barrens. In this study, we used a 14-year subtidal monitoring dataset of invertebrates, algae, and fishes to explore changes in community structure associated with the loss of forests. We found that the spatial mosaic of barrens and forests resulted in a region-wide shift in community structure. However, the magnitude of kelp forest loss and taxonomic-level consequences were spatially heterogeneous. Taxonomic diversity declined across the region, but there were no declines in richness for any group, suggesting compositional redistribution. Baseline ecological and environmental conditions, and sea urchin behaviour, explained the persistence of forests through multiple stressors. These results indicate that spatial heterogeneity in preexisting ecological and environmental conditions can explain patterns of community change.


Assuntos
Ecossistema , Kelp , Animais , Cadeia Alimentar , Florestas , Invertebrados , Ouriços-do-Mar
6.
Circ Res ; 130(4): 552-565, 2022 02 18.
Artigo em Inglês | MEDLINE | ID: mdl-35175838

RESUMO

Cardiovascular disease is a leading cause of morbidity and mortality in males and females in the United States and globally. Cardiac rehabilitation (CR) is recommended by the American Heart Association/American College of Cardiology for secondary prevention for patients with cardiovascular disease. CR participation is associated with improved cardiovascular disease risk factor management, quality of life, and exercise capacity as well as reductions in hospital admissions and mortality. Despite these advantageous clinical outcomes, significant sex disparities exist in outpatient phase II CR programming. This article reviews sex differences that are present in the spectrum of care provided by outpatient phase II CR programming (ie, from referral to clinical management). We first review CR participation by detailing the sex disparities in the rates of CR referral, enrollment, and completion. In doing so, we discuss patient, health care provider, and social/environmental level barriers to CR participation with a particular emphasis on those barriers that majorly impact females. We also evaluate sex differences in the core components incorporated into CR programming (eg, patient assessment, exercise training, hypertension management). Next, we review strategies to mitigate these sex differences in CR participation with a focus on automatic CR referral, female-only CR programming, and hybrid CR. Finally, we outline knowledge gaps and areas of future research to minimize and prevent sex differences in CR programming.


Assuntos
Reabilitação Cardíaca/métodos , Doenças Cardiovasculares/terapia , Caracteres Sexuais , Reabilitação Cardíaca/tendências , Doenças Cardiovasculares/diagnóstico , Doenças Cardiovasculares/fisiopatologia , Dieta Saudável/métodos , Exercício Físico , Feminino , Humanos , Masculino , Abandono do Hábito de Fumar/métodos , Resultado do Tratamento , Redução de Peso/fisiologia
7.
J Neuropsychiatry Clin Neurosci ; : appineuropsych20230174, 2024 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-38720623

RESUMO

OBJECTIVE: Generalized periodic discharges are a repeated and generalized electroencephalography (EEG) pattern that can be seen in the context of altered mental status. This article describes a series of five individuals with generalized periodic discharges who demonstrated signs and symptoms of catatonia, a treatable neuropsychiatric condition. METHODS: Inpatients with a clinical diagnosis of catatonia, determined with the Bush-Francis Catatonia Rating Scale (BFCRS), and EEG recordings with generalized periodic discharges were analyzed in a retrospective case series. RESULTS: Five patients with catatonia and generalized periodic discharges on EEG were evaluated from among 106 patients with catatonia and contemporaneous EEG measurements. Four of these patients showed an improvement in catatonia severity when treated with benzodiazepines, with an average reduction of 6.75 points on the BFCRS. CONCLUSIONS: Among patients with generalized periodic discharges, catatonia should be considered, in the appropriate clinical context. Patients with generalized periodic discharges and catatonia may benefit from treatment with empiric trials of benzodiazepines.

8.
Prehosp Emerg Care ; : 1-5, 2024 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-38776421

RESUMO

OBJECTIVES: Despite limited supporting data, hospitals continue to apply ambulance diversion (AD). Thus, we examined the impact of three different diversion policies on diversion hours, transport time (TT; leaving scene to arrival at the hospital), and ambulance patient offload time (APOT; arrival at the hospital to patient turnover to hospital staff) for 9-1-1 transports in a 22-hospital county Emergency Medical Services (EMS) system. METHODS: This retrospective study evaluated metrics during periods of three AD policies, each 27 days long: hospital-initiated (Period 1), complete suspension (Period 2), and County EMS-initiated (Period 3). We described the median transports and diversion hours, and compared the daily average and daily 90th percentile TT and APOT during the three study periods. RESULTS: Over the study period, there were 50,992 total transports in the county; Period 3 had fewer median transports per day than Period 1 (581 vs 623, p < 0.001), while Period 2 was similar to Period 1 (606 vs 623, p = 0.108). Median average daily diversion hours decreased from 98.1 h during Period 1 to zero hours during both Periods 2 (p < 0.001) and 3 (p < 0.001). Median daily average TT decreased from 18.3 min in Period 1 to 16.9 min in both Periods 2 (p < 0.001) and 3 (p < 0.001). Median daily 90th percentile TT showed a similar decrease from 30.2 min in Period 1 to 27.5 in Period 2 (p < 0.001), and to 28.1 in Period 3 (p = 0.001). Median average daily APOT was 26.0 min during Period 1, similar at 25.2 min during Period 2 (p = 0.826) and decreased to 20.4 min during Period 3 (p < 0.001). The median daily 90th percentile APOT was 53.9 min during Period 1, similar at 51.7 min during Period 2 (p = 0.553) and decreased to 40.3 min during Period 3 (p < 0.001). CONCLUSIONS: Compared to hospital-initiated AD, enacting no AD or County EMS-initiated AD was associated with less diversion time; TT and APOT showed statistically significant improvement without hospital-initiated AD but were of unclear clinical significance. EMS-initiated AD was difficult to interpret as that period had significantly fewer transports. EMS systems should consider these findings when developing strategies to improve TT, APOT, and system use of diversion.

9.
Proc Natl Acad Sci U S A ; 118(11)2021 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-33836567

RESUMO

Consumer and predator foraging behavior can impart profound trait-mediated constraints on community regulation that scale up to influence the structure and stability of ecosystems. Here, we demonstrate how the behavioral response of an apex predator to changes in prey behavior and condition can dramatically alter the role and relative contribution of top-down forcing, depending on the spatial organization of ecosystem states. In 2014, a rapid and dramatic decline in the abundance of a mesopredator (Pycnopodia helianthoides) and primary producer (Macrocystis pyrifera) coincided with a fundamental change in purple sea urchin (Strongylocentrotus purpuratus) foraging behavior and condition, resulting in a spatial mosaic of kelp forests interspersed with patches of sea urchin barrens. We show that this mosaic of adjacent alternative ecosystem states led to an increase in the number of sea otters (Enhydra lutris nereis) specializing on urchin prey, a population-level increase in urchin consumption, and an increase in sea otter survivorship. We further show that the spatial distribution of sea otter foraging efforts for urchin prey was not directly linked to high prey density but rather was predicted by the distribution of energetically profitable prey. Therefore, we infer that spatially explicit sea otter foraging enhances the resistance of remnant forests to overgrazing but does not directly contribute to the resilience (recovery) of forests. These results highlight the role of consumer and predator trait-mediated responses to resource mosaics that are common throughout natural ecosystems and enhance understanding of reciprocal feedbacks between top-down and bottom-up forcing on the regional stability of ecosystems.


Assuntos
Ecossistema , Comportamento Alimentar , Cadeia Alimentar , Lontras/fisiologia , Ouriços-do-Mar , Animais , Densidade Demográfica , Comportamento Predatório
10.
Proc Natl Acad Sci U S A ; 118(35)2021 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-34429359

RESUMO

Mesopredator release theory suggests that dominant predators suppress subordinate carnivores and ultimately shape community dynamics, but the assumption that subordinate species are only negatively affected ignores the possibility of facilitation through scavenging. We examined the interplay within a carnivore community consisting of cougars, coyotes, black bears, and bobcats using contemporaneous Global Positioning System telemetry data from 51 individuals; diet analysis from 972 DNA-metabarcoded scats; and data from 128 physical investigations of cougar kill sites, 28 of which were monitored with remote cameras. Resource provisioning from competitively dominant cougars to coyotes through scavenging was so prolific as to be an overwhelming determinant of coyote behavior, space use, and resource acquisition. This was evident via the strong attraction of coyotes to cougar kill sites, frequent scavenging of cougar-killed prey, and coyote diets that nearly matched cougars in the magnitude of ungulate consumption. Yet coyotes were often killed by cougars and used space to minimize encounters, complicating the fitness benefits gained from scavenging. We estimated that 23% (95% CI: 8 to 55%) of the coyote population in our study area was killed by cougars annually, suggesting that coyote interactions with cougars are a complex behavioral game of risk and reward. In contrast, we found no indication that bobcat space use or diet was influenced by cougars. Black bears avoided cougars, but there was no evidence of attraction to cougar kill sites and much lower levels of ungulate consumption and carcass visitation than for coyotes. Interspecific interactions among carnivores are multifaceted, encompassing both suppression and facilitation.


Assuntos
Coiotes/fisiologia , Cadeia Alimentar , Lynx/fisiologia , Comportamento Predatório , Puma/fisiologia , Recompensa , Ursidae/fisiologia , Animais , Carnívoros/fisiologia , Ecossistema , Dinâmica Populacional
11.
BMC Med Inform Decis Mak ; 22(Suppl 2): 348, 2024 Mar 03.
Artigo em Inglês | MEDLINE | ID: mdl-38433189

RESUMO

BACKGROUND: Systemic lupus erythematosus (SLE) is a rare autoimmune disorder characterized by an unpredictable course of flares and remission with diverse manifestations. Lupus nephritis, one of the major disease manifestations of SLE for organ damage and mortality, is a key component of lupus classification criteria. Accurately identifying lupus nephritis in electronic health records (EHRs) would therefore benefit large cohort observational studies and clinical trials where characterization of the patient population is critical for recruitment, study design, and analysis. Lupus nephritis can be recognized through procedure codes and structured data, such as laboratory tests. However, other critical information documenting lupus nephritis, such as histologic reports from kidney biopsies and prior medical history narratives, require sophisticated text processing to mine information from pathology reports and clinical notes. In this study, we developed algorithms to identify lupus nephritis with and without natural language processing (NLP) using EHR data from the Northwestern Medicine Enterprise Data Warehouse (NMEDW). METHODS: We developed five algorithms: a rule-based algorithm using only structured data (baseline algorithm) and four algorithms using different NLP models. The first NLP model applied simple regular expression for keywords search combined with structured data. The other three NLP models were based on regularized logistic regression and used different sets of features including positive mention of concept unique identifiers (CUIs), number of appearances of CUIs, and a mixture of three components (i.e. a curated list of CUIs, regular expression concepts, structured data) respectively. The baseline algorithm and the best performing NLP algorithm were externally validated on a dataset from Vanderbilt University Medical Center (VUMC). RESULTS: Our best performing NLP model incorporated features from both structured data, regular expression concepts, and mapped concept unique identifiers (CUIs) and showed improved F measure in both the NMEDW (0.41 vs 0.79) and VUMC (0.52 vs 0.93) datasets compared to the baseline lupus nephritis algorithm. CONCLUSION: Our NLP MetaMap mixed model improved the F-measure greatly compared to the structured data only algorithm in both internal and external validation datasets. The NLP algorithms can serve as powerful tools to accurately identify lupus nephritis phenotype in EHR for clinical research and better targeted therapies.


Assuntos
Lúpus Eritematoso Sistêmico , Nefrite Lúpica , Humanos , Nefrite Lúpica/diagnóstico , Registros Eletrônicos de Saúde , Processamento de Linguagem Natural , Fenótipo , Doenças Raras
12.
J ECT ; 2024 Jan 25.
Artigo em Inglês | MEDLINE | ID: mdl-38265759

RESUMO

OBJECTIVES: The objective study was to investigate the safety and efficacy of electroconvulsive therapy (ECT) in a retrospective cohort of pediatric patients. METHODS: A single-site retrospective analysis was conducted of patients aged younger than 18 years who received ECT in a private university hospital from January 28, 2012 to April 8, 2023. Treatment efficacy and adverse events were determined retrospectively through review of the medical record. RESULTS: A total of 36 pediatric patients met the inclusion criteria. Catatonia was the most common presenting indication for ECT, followed by psychosis and suicidal ideation. For all patients, Clinical Global Impressions-Improvement scale scores indicated that it was very likely for a subject to experience at least "much improvement" with the estimated probability of receiving a Clinical Global Impressions-Improvement scale score better than 3 of 0.852 (t.s. = 16.3; P < 0.001; 95% confidence interval, 0.711-0.931). All patients with catatonia demonstrated a positive clinical response and experienced a statistically significant reduction in total Bush-Francis Catatonia Rating Scale scores observed (t = 11.9; df = 20; SD = 6.3; P < 0.001; 95% confidence interval, 12.6-17.9). No significant adverse events were reported for any patient in the cohort. However, 14 (38.9%) patients experienced prolonged seizures, all of which were terminated with propofol (mean, 49.7 mg). CONCLUSIONS: This study provides further data supporting the safe and effective use of pediatric ECT in the treatment of various psychiatric conditions. However, more research is needed to determine the risk factors associated with prolonged seizures and the optimal seizure parameters in young people.

13.
J Neurosci ; 42(9): 1679-1691, 2022 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-35101966

RESUMO

Myelin is essential to neuronal health and CNS function, and oligodendrocytes (OLs) undergo a complex process of cytoskeletal remodeling to form compact myelin sheaths. We previously discovered that a formin protein, Dishevelled associated activator of morphogenesis 2 (Daam2), suppresses OL differentiation through Wnt signaling; however, its role in cytoskeletal control remains unknown. To investigate this, we used OL-specific Daam2 conditional knockout (Daam2 cKO) mice of either sex and found myelin decompaction during an active period of myelination in postnatal development and motor coordination deficits in adulthood. Using primary OL cultures, we found Daam2-depleted OLs showed morphologic dysregulation during differentiation, suggesting that Daam2 regulates the OL cytoskeleton. In vivo screening identified the actin regulators Rac1 and Gelsolin as possible effectors in Daam2-deficient OL cytoskeletal regulation. Using gain-of-function and loss-of-function (LOF) experiments in primary OLs, we found that Rac1 and Gelsolin operate downstream of Daam2 in OL differentiation, with Gelsolin and Daam2 promoting and inhibiting membrane spreading during late differentiation, respectively. In vivo experiments using Daam2 cKO mice revealed increased protein levels of Gelsolin in the developing white matter with no change in RNA levels, suggesting that Daam2 acts in a posttranslational manner to suppress Gelsolin levels. In vitro biochemical studies show Daam2 induces Gelsolin ubiquitination and degradation in OLs. Together, our studies show Daam2 is essential for formation of functional myelin through modulation of Gelsolin levels to regulate the OL cytoskeleton. These findings further demonstrate the critical role of cytoskeletal dynamics in myelination and reveal novel avenues for treatment of a variety of white matter diseases.SIGNIFICANCE STATEMENT Proper myelin formation is essential to CNS function, and oligodendrocytes (OLs) require extensive changes in the actin cytoskeleton to form myelin sheaths. Here, we show that the formin protein Dishevelled associated activator of morphogenesis 2 (Daam2) is necessary for myelin compaction during development and motor learning in adulthood. Further, we demonstrate that Daam2 regulates OL differentiation and morphology through actin regulators Rac1 and Gelsolin. Lastly, we find that Daam2 may control myelin compaction by modulating the ubiquitination and degradation of Gelsolin through recruitment of the E3 ubiquitin ligase Nedd4. These findings reveal novel pathways for regulating myelin structure and function during white matter development.


Assuntos
Citoesqueleto de Actina , Gelsolina , Proteínas dos Microfilamentos , Bainha de Mielina , Neuropeptídeos , Oligodendroglia , Proteínas rac1 de Ligação ao GTP , Proteínas rho de Ligação ao GTP , Citoesqueleto de Actina/metabolismo , Actinas/metabolismo , Animais , Diferenciação Celular , Gelsolina/genética , Gelsolina/metabolismo , Camundongos , Proteínas dos Microfilamentos/metabolismo , Bainha de Mielina/metabolismo , Neuropeptídeos/metabolismo , Oligodendroglia/citologia , Oligodendroglia/metabolismo , Proteínas rac1 de Ligação ao GTP/metabolismo , Proteínas rho de Ligação ao GTP/metabolismo
14.
Int J Obes (Lond) ; 47(2): 109-116, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36463326

RESUMO

BACKGROUND/OBJECTIVES: Obesity, defined as excessive fat accumulation that represents a health risk, is increasing in adults and children, reaching global epidemic proportions. Body mass index (BMI) correlates with body fat and future health risk, yet differs in prediction by fat distribution, across populations and by age. Nonetheless, few genetic studies of BMI have been conducted in ancestrally diverse populations. Gene expression association with BMI was assessed in the Multi-Ethnic Study of Atherosclerosis (MESA) in four self-identified race and ethnicity (SIRE) groups to identify genes associated with obesity. SUBJECTS/METHODS: RNA-sequencing was performed on 1096 MESA participants (37.8% white, 24.3% Hispanic, 28.4% African American, and 9.5% Chinese American) and linear models were used to assess the association of expression from each gene for its effect on BMI, adjusting for age, sex, sequencing center, study site, five expression and four genetic principal components in each self-identified race group. Sample-size-weighted meta-analysis was performed to identify genes with BMI-associated expression across ancestry groups. RESULTS: Within individual SIRE groups, there were zero to three genes whose expression is significantly (p < 1.97 × 10-6) associated with BMI. Across all groups, 45 genes were identified by meta-analysis whose expression was significantly associated with BMI, explaining 29.7% of BMI variation. The 45 genes are expressed in a variety of tissues and cell types and are enriched for obesity-related processes including erythrocyte function, oxygen binding and transport, and JAK-STAT signaling. CONCLUSIONS: We have identified genes whose expression is significantly associated with obesity in a multi-ethnic cohort. We have identified novel genes associated with BMI as well as confirmed previously identified genes from earlier genetic analyses. These novel genes and their biological pathways represent new targets for understanding the biology of obesity as well as new therapeutic intervention to reduce obesity and improve global public health.


Assuntos
Índice de Massa Corporal , Expressão Gênica , Obesidade , Adulto , Criança , Humanos , Aterosclerose , Obesidade/epidemiologia , Obesidade/genética
15.
Brief Bioinform ; 22(6)2021 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-34015820

RESUMO

Large datasets of hundreds to thousands of individuals measuring RNA-seq in observational studies are becoming available. Many popular software packages for analysis of RNA-seq data were constructed to study differences in expression signatures in an experimental design with well-defined conditions (exposures). In contrast, observational studies may have varying levels of confounding transcript-exposure associations; further, exposure measures may vary from discrete (exposed, yes/no) to continuous (levels of exposure), with non-normal distributions of exposure. We compare popular software for gene expression-DESeq2, edgeR and limma-as well as linear regression-based analyses for studying the association of continuous exposures with RNA-seq. We developed a computation pipeline that includes transformation, filtering and generation of empirical null distribution of association P-values, and we apply the pipeline to compute empirical P-values with multiple testing correction. We employ a resampling approach that allows for assessment of false positive detection across methods, power comparison and the computation of quantile empirical P-values. The results suggest that linear regression methods are substantially faster with better control of false detections than other methods, even with the resampling method to compute empirical P-values. We provide the proposed pipeline with fast algorithms in an R package Olivia, and implemented it to study the associations of measures of sleep disordered breathing with RNA-seq in peripheral blood mononuclear cells in participants from the Multi-Ethnic Study of Atherosclerosis.


Assuntos
Benchmarking/métodos , RNA-Seq , Análise de Sequência de RNA , Software , Algoritmos , Aterosclerose/epidemiologia , Aterosclerose/etiologia , Aterosclerose/metabolismo , Simulação por Computador , Suscetibilidade a Doenças , Predisposição Genética para Doença , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Mutação , Fenótipo , Medição de Risco , Fatores de Risco , Navegador
16.
BMC Microbiol ; 23(1): 235, 2023 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-37626313

RESUMO

BACKGROUND: Staphylococcus aureus can infect and adapt to multiple host species. However, our understanding of the genetic and evolutionary drivers of its generalist lifestyle remains inadequate. This is particularly important when considering local populations of S. aureus, where close physical proximity between bacterial lineages and between host species may facilitate frequent and repeated interactions between them. Here, we aim to elucidate the genomic differences between human- and animal-derived S. aureus from 437 isolates sampled from disease cases in the northeast region of the United States. RESULTS: Multi-locus sequence typing revealed the existence of 75 previously recognized sequence types (ST). Our population genomic analyses revealed heterogeneity in the accessory genome content of three dominant S. aureus lineages (ST5, ST8, ST30). Genes related to antimicrobial resistance, virulence, and plasmid types were differentially distributed among isolates according to host (human versus non-human) and among the three major STs. Across the entire population, we identified a total of 1,912 recombination events that occurred in 765 genes. The frequency and impact of homologous recombination were comparable between human- and animal-derived isolates. Low-frequency STs were major donors of recombined DNA, regardless of the identity of their host. The most frequently recombined genes (clfB, aroA, sraP) function in host infection and virulence, which were also frequently shared between the rare lineages. CONCLUSIONS: Taken together, these results show that frequent but variable patterns of recombination among co-circulating S. aureus lineages, including the low-frequency lineages, that traverse host barriers shape the structure of local gene pool and the reservoir of host-associated genetic variants. Our study provides important insights to the genetic and evolutionary factors that contribute to the ability of S. aureus to colonize and cause disease in multiple host species. Our study highlights the importance of continuous surveillance of S. aureus circulating in different ecological host niches and the need to systematically sample from them. These findings will inform development of effective measures to control S. aureus colonization, infection, and transmission across the One Health continuum.


Assuntos
Pool Gênico , Infecções Estafilocócicas , Animais , Tipagem de Sequências Multilocus , Staphylococcus aureus/genética , Evolução Biológica
17.
Glob Chang Biol ; 29(19): 5634-5651, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37439293

RESUMO

Marine protected areas (MPAs) have gained attention as a conservation tool for enhancing ecosystem resilience to climate change. However, empirical evidence explicitly linking MPAs to enhanced ecological resilience is limited and mixed. To better understand whether MPAs can buffer climate impacts, we tested the resistance and recovery of marine communities to the 2014-2016 Northeast Pacific heatwave in the largest scientifically designed MPA network in the world off the coast of California, United States. The network consists of 124 MPAs (48 no-take state marine reserves, and 76 partial-take or special regulation conservation areas) implemented at different times, with full implementation completed in 2012. We compared fish, benthic invertebrate, and macroalgal community structure inside and outside of 13 no-take MPAs across rocky intertidal, kelp forest, shallow reef, and deep reef nearshore habitats in California's Central Coast region from 2007 to 2020. We also explored whether MPA features, including age, size, depth, proportion rock, historic fishing pressure, habitat diversity and richness, connectivity, and fish biomass response ratios (proxy for ecological performance), conferred climate resilience for kelp forest and rocky intertidal habitats spanning 28 MPAs across the full network. Ecological communities dramatically shifted due to the marine heatwave across all four nearshore habitats, and MPAs did not facilitate habitat-wide resistance or recovery. Only in protected rocky intertidal habitats did community structure significantly resist marine heatwave impacts. Community shifts were associated with a pronounced decline in the relative proportion of cold water species and an increase in warm water species. MPA features did not explain resistance or recovery to the marine heatwave. Collectively, our findings suggest that MPAs have limited ability to mitigate the impacts of marine heatwaves on community structure. Given that mechanisms of resilience to climate perturbations are complex, there is a clear need to expand assessments of ecosystem-wide consequences resulting from acute climate-driven perturbations, and the potential role of regulatory protection in mitigating community structure changes.


Assuntos
Ecossistema , Kelp , Animais , Conservação dos Recursos Naturais/métodos , Biomassa , Invertebrados , Florestas , Peixes
18.
Phys Rev Lett ; 131(17): 171401, 2023 Oct 27.
Artigo em Inglês | MEDLINE | ID: mdl-37955496

RESUMO

Coating thermal noise is one of the dominant noise sources in current gravitational wave detectors and ultimately limits their ability to observe weaker or more distant astronomical sources. This Letter presents investigations of TiO_{2} mixed with SiO_{2} (TiO_{2}:SiO_{2}) as a coating material. We find that, after heat treatment for 100 h at 850 °C, thermal noise of a highly reflective coating comprising of TiO_{2}:SiO_{2} and SiO_{2} reduces to 76% of the current levels in the Advanced LIGO and Advanced Virgo detectors-with potential for reaching 45%, if we assume the mechanical loss of state-of-the-art SiO_{2} layers. Furthermore, those coatings show low optical absorption of <1 ppm and optical scattering of ≲5 ppm. Notably, we still observe excellent optical and thermal noise performance following crystallization in the coatings. These results show the potential to meet the parameters required for the next upgrades of the Advanced LIGO and Advanced Virgo detectors.

19.
Chemistry ; 29(45): e202301188, 2023 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-37249243

RESUMO

Mononuclear copper(II)-phenanthroline complexes have been widely investigated as anticancer agents whereas multinuclear copper(II)-phenanthroline complexes are underexplored. Here the synthesis and characterisation of two new binuclear copper(II)-phenanthroline complexes 1 and 2 is reported, comprising of 2,9-dimethyl-1,10-phenanthroline or 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline, terminal chloride ligands, and bridging chloride or hydroxide ligands. The binuclear copper(II) complex containing 2,9-dimethyl-1,10-phenanthroline 1 displays nanomolar toxicity towards bulk breast cancer cells and breast cancer stem cells (CSCs) grown in monolayers, >50-fold greater than cisplatin (an anticancer metallodrug) and salinomycin (a gold-standard anti-CSC agent). Spectacularly, 1 exhibits >100-fold greater potency toward three-dimensionally cultured mammospheres than cisplatin and salinomycin. Mechanistic studies show that 1 evokes breast CSC apoptosis by elevating intracellular reactive oxygen species levels and damaging genomic DNA (possibly by an oxidative mechanism). To the best of our knowledge, this is the first study to probe the anti-breast CSC properties of binuclear copper(II)-phenanthroline complexes.


Assuntos
Antineoplásicos , Neoplasias da Mama , Complexos de Coordenação , Humanos , Feminino , Cisplatino , Cobre , Fenantrolinas/farmacologia , Linhagem Celular Tumoral , Complexos de Coordenação/farmacologia , Neoplasias da Mama/tratamento farmacológico , Cloretos , Ligantes , Antineoplásicos/farmacologia , Células-Tronco Neoplásicas
20.
Curr Atheroscler Rep ; 25(6): 247-256, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-37040008

RESUMO

PURPOSE OF REVIEW: To review the benefits, challenges, and advances in cardiac rehabilitation (CR) in the management of cardiovascular disease (CVD). RECENT FINDINGS: Novel strategies of delivering CR are being studied that use remote technologies to link patients with CR professionals. These strategies used alone or in tandem with center-based, face-to-face strategies appear to have shorter-term effectiveness, but additional work is needed to assess the longer-term impact. Cardiac rehabilitation improves patient outcomes, but only a minority of eligible individuals participate. Solutions exist to help bridge the barriers to CR participation, including systematic solutions, such as automatic CR referral of eligible patients. Efforts are underway to improve participation, improve the effectiveness of CR therapies, and enhance the reach of CR into new patient groups. Future work in the field is focused on opportunities to advance the science, practice, and policies that will shape and improve the delivery and impact of CR services.


Assuntos
Reabilitação Cardíaca , Doenças Cardiovasculares , Humanos , Terapia por Exercício , Prevenção Secundária
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